<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
<p>Hi Smith,<br>
</p>
<div class="moz-cite-prefix"><br>
</div>
<blockquote type="cite"
cite="mid:80461477.1007756.1616167642770@mail.yahoo.com">
<div class="ydpfd3a6039yahoo-style-wrap"
style="font-family:Helvetica Neue, Helvetica, Arial,
sans-serif;font-size:13px;">
<div dir="ltr" data-setdir="false">
<div dir="ltr" data-setdir="false">
<div dir="ltr"><span>By clicking "phenix" in my centos 8
terminal, the phenix GUI can be launched, but in the
terminal there were messages "<span>Gtk-Message:
11:08:21.204: Failed to load module "pk-gtk-module"
and message "<span>Gtk-Message: 11:08:21.205: Failed
to load module "canberra-gtk-module". Does this mean
I have failed for something for my phenix
installation? Which phenix functions it affects? Is
any way I install these uninstalled modules at this
stage and how to install?</span></span></span></div>
</div>
</div>
</div>
</blockquote>
<p>it's just noise. Don't worry about it. Things should work,
normally.</p>
<blockquote type="cite"
cite="mid:80461477.1007756.1616167642770@mail.yahoo.com">
<div class="ydpfd3a6039yahoo-style-wrap"
style="font-family:Helvetica Neue, Helvetica, Arial,
sans-serif;font-size:13px;">
<div dir="ltr" data-setdir="false">
<div dir="ltr" data-setdir="false">
<div dir="ltr"><span><span><span>Next, when I run the
phenix.real_space_refine as command line in the
terminal, it wroks fine. However when I run it in
the phenix GUI, I got the following assertion error
message (see following between "----").</span></span></span></div>
<div dir="ltr"><span><span><span><br clear="none">
</span></span></span></div>
<div dir="ltr"><span><span><span>I am looking forward to
getting your reply to have the above issues solved.</span></span></span></div>
</div>
</div>
</div>
</blockquote>
<p>We fixed this problem already. Please use the most recent version
of Phenix located in usual place:</p>
<p><a class="moz-txt-link-freetext" href="http://phenix-online.org/download/nightly_builds.cgi">http://phenix-online.org/download/nightly_builds.cgi</a></p>
<p>Let us know of any other issues!</p>
<p>Pavel<br>
</p>
<p><br>
</p>
<blockquote type="cite"
cite="mid:80461477.1007756.1616167642770@mail.yahoo.com">
<div class="ydpfd3a6039yahoo-style-wrap"
style="font-family:Helvetica Neue, Helvetica, Arial,
sans-serif;font-size:13px;">
<div dir="ltr" data-setdir="false">
<div dir="ltr" data-setdir="false">
<div dir="ltr"><span><span><span><br clear="none">
</span></span></span></div>
<div dir="ltr"><span><span><span>Best wishes,</span></span></span></div>
<div dir="ltr"><span><span><span><br clear="none">
</span></span></span></div>
<div dir="ltr"><span><span><span>Smith</span></span></span></div>
<div dir="ltr"><span><span><span><br clear="none">
</span></span></span></div>
<div dir="ltr"><span><span><span>----</span></span></span></div>
<span><span></span></span><br clear="none">
AssertionError : <br clear="none">
Traceback:<br clear="none">
File
"/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/cctbx_project/libtbx/runtime_utils.py",
line 181, in run<br clear="none">
return_value = self.target()<br clear="none">
<br clear="none">
File
"/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/cctbx_project/libtbx/runtime_utils.py",
line 76, in __call__<br clear="none">
result = self.run()<br clear="none">
<br clear="none">
File
"/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/phenix/wxGUI2/program_template/real_space_refine.py",
line 52, in run<br clear="none">
self.result.validation_cryoem = self.run_validation()<br
clear="none">
<br clear="none">
File
"/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/phenix/wxGUI2/program_template/real_space_refine.py",
line 113, in run_validation<br clear="none">
task.validate()<br clear="none">
<br clear="none">
File
"/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/phenix/phenix/programs/validation_cryoem.py",
line 476, in validate<br clear="none">
self.params.map_model_cc.ignore_symmetry_conflicts)<br
clear="none">
<br clear="none">
File
"/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/cctbx_project/iotbx/map_model_manager.py",
line 302, in __init__<br clear="none">
mmmn.shift_origin()<br clear="none">
<br clear="none">
File
"/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/cctbx_project/iotbx/map_model_manager.py",
line 7837, in shift_origin<br clear="none">
assert approx_equal(existing_shift_cart,
expected_model_shift_cart)<br clear="none">
<br clear="none">
<br clear="none">
<br clear="none">
Platform info:<br clear="none">
__FILE__ =
/dev/shm/bkpoon/software/release/patch/modules/cctbx_project/boost_adaptbx/meta_ext.cpp<br
clear="none">
__DATE__ = Jan 21 2021<br clear="none">
__TIME__ = 11:15:23<br clear="none">
__TIMESTAMP__ = Mon Oct 5 22:43:41 2020<br clear="none">
__x86_64__<br clear="none">
__linux<br clear="none">
__GNUC__ = 4<br clear="none">
__GNUC_MINOR__ = 4<br clear="none">
__GNUC_PATCHLEVEL__ = 7<br clear="none">
__GXX_WEAK__ = 1<br clear="none">
__LP64__ = 1<br clear="none">
__VERSION__ = 4.4.7 20120313 (Red Hat 4.4.7-23)<br
clear="none">
FE_INEXACT = 32<br clear="none">
FE_DIVBYZERO = 4<br clear="none">
FE_UNDERFLOW = 16<br clear="none">
FE_OVERFLOW = 8<br clear="none">
FE_INVALID = 1<br clear="none">
FE_ALL_EXCEPT = 61<br clear="none">
__SSE2__ = 1<br clear="none">
BOOST_LIB_VERSION = 1_70<br clear="none">
PY_VERSION = 2.7.15<br clear="none">
PYTHON_API_VERSION = 1013<br clear="none">
sizeof(bool) = 1<br clear="none">
sizeof(short) = 2<br clear="none">
sizeof(int) = 4<br clear="none">
sizeof(long) = 8<br clear="none">
sizeof(std::size_t) = 8<br clear="none">
sizeof(void*) = 8<br clear="none">
sizeof(long long) = 8<br clear="none">
sizeof(float) = 4<br clear="none">
sizeof(double) = 8<br clear="none">
sizeof(long double) = 16<br clear="none">
sizeof(boost::int32_t) = 4<br clear="none">
sizeof(boost::uint32_t) = 4<br clear="none">
sizeof(wchar_t) = 4<br clear="none">
__PTRDIFF_TYPE__<br clear="none">
Py_USING_UNICODE<br clear="none">
sizeof(PY_UNICODE_TYPE) = 4<br clear="none">
_OPENMP = 200805<br clear="none">
gnu libc version: 2.28<br clear="none">
BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG<br
clear="none">
boost/TAG: None<br clear="none">
os.name: posix<br clear="none">
sys.platform: linux2<br clear="none">
sys.byteorder: little<br clear="none">
platform.platform():
Linux-4.18.0-193.28.1.el8_2.x86_64-x86_64-with-centos-8.2.2004-Core<br
clear="none">
platform.architecture(): ('64bit', '')<br clear="none">
floating_point_exceptions.division_by_zero_trapped: False<br
clear="none">
floating_point_exceptions.invalid_trapped: False<br
clear="none">
floating_point_exceptions.overflow_trapped: False<br
clear="none">
number of processors: 12<br clear="none">
Memory total: 134,367,047,680<br clear="none">
Memory free: 124,477,964,288<br clear="none">
import thread: OK<br clear="none">
"hello" = ['h', 'e', 'l', 'l', 'o']<br clear="none">
u"hello" = ['h', '\x00', '\x00', '\x00', 'e', '\x00',
'\x00', '\x00', 'l', '\x00', '\x00', '\x00', 'l', '\x00',
'\x00', '\x00', 'o', '\x00', '\x00', '\x00']<br clear="none">
u"\u00C5" = ['\xc5', '\x00', '\x00', '\x00'] as utf-8 =
['\xc3', '\x85']<br clear="none">
LATIN CAPITAL LETTER A WITH RING ABOVE = Å<br clear="none">
</div>
<div><br>
</div>
</div>
<div><br>
</div>
</div>
<div id="yahoo_quoted_6877009528" class="yahoo_quoted">
<div style="font-family:'Helvetica Neue', Helvetica, Arial,
sans-serif;font-size:13px;color:#26282a;">
<div> On Thursday, March 18, 2021, 6:36:32 AM GMT+8, Pavel
Afonine <a class="moz-txt-link-rfc2396E" href="mailto:pafonine@lbl.gov"><pafonine@lbl.gov></a> wrote: </div>
<div><br>
</div>
<div><br>
</div>
<div>
<div id="yiv3918597431">
<div>
<p>Hi Smith,</p>
<p>all data files that are used in tutorials are shipped
with Phenix. So you don't need to download anything
additionally. If you want to use your own data, just
do it and follow the tutorial script. In this case
your files have the same property as in the tutorial
(for example, have symmetry if it is used as part of
the tutorial).</p>
<p>Hope this helps!</p>
<p>Pavel<br clear="none">
</p>
<div class="yiv3918597431yqt1414037113"
id="yiv3918597431yqt74033">
<div class="yiv3918597431moz-cite-prefix">On 3/13/21
18:29, Smith Lee wrote:<br clear="none">
</div>
<blockquote type="cite"> </blockquote>
</div>
</div>
<div class="yiv3918597431yqt1414037113"
id="yiv3918597431yqt53980">
<div>
<div class="yiv3918597431yahoo-style-wrap"
style="font-family:Helvetica Neue, Helvetica, Arial,
sans-serif;font-size:13px;">
<div dir="ltr">Dear All,</div>
<div dir="ltr"><br clear="none">
</div>
<div dir="ltr">
<div dir="ltr">For "<span>Tutorial: Solving a
structure with cryo-EM data using docking", it
is easy to download the <span>emd_20026_half_map_1_box.ccp4
and emd_20026_half_map_2_box.ccp4 from the
emd-20026 depositation, but will you please
let me know step by step how to get the
tutorial used <span>seq.dat, <span>20026_auto_sharpen_A.ccp4
(any other name for this file? Cannot
find the exact name file in emd_20026 <span><span><span>depositation</span></span></span>),
<span>apoferritin_chainA_rsr.pdb (it
mentioned "<span>model refined against
sharpened map", which sharpened map,
and what was the refinement method
ued?</span>), </span></span></span></span></span><span></span><span>run_denmod_dock.csh?</span></div>
<div dir="ltr"><span><br clear="none">
</span></div>
<div dir="ltr"><span>I am looking forward to
getting your reply.</span></div>
<div dir="ltr"><span><br clear="none">
</span></div>
<div dir="ltr"><span>Best wishes,</span></div>
<div dir="ltr"><span><br clear="none">
</span></div>
<div dir="ltr"><span>Smith<br clear="none">
</span></div>
<div dir="ltr"><span></span><br clear="none">
</div>
</div>
</div>
<br clear="none">
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</body>
</html>